Find an ungapped pattern window from a set of protein sequences

This program is to find an ungapped pattern window of certain width from a set of protein sequences

This program is a bioinformatics tool developed for helping biologists finding patterns from a set of protein sequences. The method is the first one that fully utilizes the advantages of the Dirichlet mixture models. It starts from a random pattern and iteratively improves the Bayesian log-odds ratio score as the pattern is updated. When the score cannot be significantly improved, the algorithm terminates and returns a pattern window of pre-specified length. The resulting pattern can be used as a starting point for later refined alignment through introducing gaps. We are developing the more advanced version that can introduce gaps into the pattern. We believe the current ungapped version is already very helpful for identifying conserved regions of the protein sequences. It is a useful tool that can save a certain amount of manual work in the pattern discovery.

To use the c program, first compile it using mex in linux/unix, then run the demo script gibbs_script_4_1.m. You can manipulate the demo script for your needs.